test mechanism changes

gkno · May 27, 2015 · ace3c44 · ace3c44
1 parent 2fa2498
commit ace3c44
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Showing 3 changed files with 13 additions and 13 deletions.
diff --git a/test/common/strip_error → test/common/strip_var b/test/common/strip_error → test/common/strip_var
diff --git a/test/decompose_blocksub/_run.sh b/test/decompose_blocksub/_run.sh
@@ -6,15 +6,16 @@ DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
 . ${DIR}/../common/_helpers.sh
 # put path to vt binary into handy variable
 VT=${DIR}/../../vt
+STRIP_VAR=${DIR}/../common/strip_var
 # immediately quit on errors
 set -e
 
 # create temporary directory and ensure cleanup on termination
-#export TMPDIR=$(mktemp -d)
 export TMPDIR=${DIR}/tmp
 mkdir -p ${TMPDIR}
 trap "set -x; rm -rf ${TMPDIR}" EXIT KILL TERM INT HUP
 
+echo "-------------------------------" >&2
 echo "Tests for vt decompose_blocksub" >&2
 echo "-------------------------------" >&2
 
@@ -24,14 +25,13 @@ echo "-------------------------------" >&2
 # ---------------------------------------------------------------------------
 
 set -x
-#mkdir -p ${TMPDIR}/01
 
 # call program
 ${VT} \
     decompose_blocksub \
     ${DIR}/01_IN_even_length.vcf \
-    >${TMPDIR}/01_OUT_even_length.vcf \
-    2> >(strip_stderr > ${TMPDIR}/01_OUT_even_length.stderr)
+    -o ${TMPDIR}/01_OUT_even_length.vcf \
+    2>&1 | ${STRIP_VAR} > ${TMPDIR}/01_OUT_even_length.stderr
 
 # compare results
 diff ${DIR}/01_OUT_even_length.vcf ${TMPDIR}/01_OUT_even_length.vcf
@@ -44,14 +44,13 @@ set +x
 # ---------------------------------------------------------------------------
 
 set -x
-#mkdir -p ${TMPDIR}/02
 
 # call program
 ${VT} \
     decompose_blocksub -a \
     ${DIR}/02_IN_uneven_length.vcf \
-    >${TMPDIR}/02_OUT_uneven_length.vcf \
-    2> >(strip_stderr > ${TMPDIR}/02_OUT_uneven_length.stderr) \
+    -o ${TMPDIR}/02_OUT_uneven_length.vcf \
+    2>&1 | ${STRIP_VAR} > ${TMPDIR}/02_OUT_uneven_length.stderr \
 
 # compare results
 diff ${DIR}/02_OUT_uneven_length.vcf ${TMPDIR}/02_OUT_uneven_length.vcf

diff --git a/test/normalize/_run.sh b/test/normalize/_run.sh
@@ -8,35 +8,36 @@ DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
 VT=${DIR}/../../vt
 # put path to vt binary into handy variable
 REF=${DIR}/../ref/20.fa.gz
+STRIP_VAR=${DIR}/../common/strip_var
 # immediately quit on errors
 set -e
 
 # create temporary directory and ensure cleanup on termination
-#export TMPDIR=$(mktemp -d)
 export TMPDIR=${DIR}/tmp
 mkdir -p ${TMPDIR}
 trap "set -x; rm -rf ${TMPDIR}" EXIT KILL TERM INT HUP
 
+echo "----------------------" >&2
 echo "Tests for vt normalize" >&2
 echo "----------------------" >&2
 
-
 # ---------------------------------------------------------------------------
 # Test 01: normalization of indels from Mills et al. chromosome 20
 # ---------------------------------------------------------------------------
 
+# call program
+
 set -x
 
-# call program
 ${VT} \
     normalize \
     ${DIR}/01_IN.vcf \
     -r ${REF} \
-    >${TMPDIR}/01_OUT.vcf \
-    2> >(strip_stderr > ${TMPDIR}/01_OUT.stderr)
+    -o ${TMPDIR}/01_OUT.vcf \
+    2>&1 | ${STRIP_VAR} > ${TMPDIR}/01_OUT.stderr
 
 # compare results
 diff ${DIR}/01_OUT.vcf ${TMPDIR}/01_OUT.vcf
 diff ${DIR}/01_OUT.stderr ${TMPDIR}/01_OUT.stderr
-
+   
 set +x